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OPENSEQ.org
1kkl_A_D
Genes: A B A+B
Length: 157 87 238
Sequences: 784 3244 379
Seq/Len: 4.99 37.29 1.59
MirrorTree (Pazo et al. 2001) 0.39
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.07 0.01 0.18
2 0.07 0.01 0.43
5 0.07 0.01 1.20
10 0.07 0.01 1.30
20 0.07 0.01 1.55
100 0.07 0.06 1.91
∞ 0.07 0.14 2.70
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
37_G 42_N 1.51 0.88 0.24
4_S 34_L 1.47 0.86 0.22
18_I 56_K 1.17 0.64 0.09
29_T 20_V 1.15 0.62 0.09
7_V 49_V 1.14 0.60 0.08
151_L 76_L 1.12 0.59 0.08
16_V 24_T 1.11 0.57 0.08
18_I 82_C 1.09 0.55 0.07
46_V 40_T 1.07 0.53 0.07
8_L 42_N 1.07 0.53 0.07
68_L 37_N 1.05 0.51 0.06
84_G 17_P 1.02 0.48 0.05
53_E 60_I 1.01 0.47 0.05
48_V 47_M 1.01 0.47 0.05
13_G 42_N 1.00 0.46 0.05
109_D 53_G 1.00 0.46 0.05
42_A 18_A 1.00 0.46 0.05
38_H 42_N 0.99 0.45 0.05
24_V 18_A 0.99 0.44 0.05
65_S 60_I 0.98 0.44 0.05
141_Y 2_Q 0.97 0.42 0.04
118_P 68_D 0.96 0.42 0.04
15_G 44_K 0.95 0.40 0.04
47_D 5_F 0.95 0.40 0.04
16_V 68_D 0.95 0.40 0.04
148_E 17_P 0.94 0.40 0.04
153_H 13_I 0.94 0.40 0.04
130_E 58_A 0.94 0.39 0.04
118_P 44_K 0.94 0.39 0.04
62_P 10_D 0.94 0.39 0.04
142_D 49_V 0.94 0.39 0.04
81_F 52_L 0.94 0.39 0.04
37_G 44_K 0.92 0.38 0.04
75_I 32_V 0.92 0.38 0.04
130_E 42_N 0.92 0.38 0.04
45_R 41_V 0.92 0.37 0.04
154_L 13_I 0.91 0.37 0.04
73_L 68_D 0.91 0.37 0.04
130_E 44_K 0.91 0.36 0.04
97_H 26_S 0.91 0.36 0.04
95_I 70_N 0.91 0.36 0.04
147_F 80_M 0.90 0.36 0.04
38_H 43_L 0.89 0.35 0.03
48_V 26_S 0.89 0.34 0.03
21_D 31_D 0.89 0.34 0.03
113_P 14_H 0.88 0.34 0.03
106_L 73_L 0.88 0.33 0.03
49_Y 6_K 0.88 0.33 0.03
46_V 59_E 0.87 0.33 0.03
22_S 2_Q 0.87 0.33 0.03
36_R 68_D 0.87 0.32 0.03
95_I 5_F 0.86 0.32 0.03
144_T 19_T 0.85 0.31 0.03
53_E 17_P 0.84 0.30 0.03
67_L 50_V 0.84 0.30 0.03
96_V 53_G 0.84 0.30 0.03
136_R 17_P 0.83 0.30 0.03
142_D 69_E 0.83 0.29 0.03
94_L 73_L 0.83 0.29 0.03
13_G 43_L 0.83 0.29 0.03
151_L 50_V 0.83 0.29 0.03
113_P 12_G 0.82 0.29 0.03
132_A 6_K 0.82 0.28 0.03
106_L 50_V 0.82 0.28 0.03
5_H 24_T 0.81 0.27 0.02
130_E 56_K 0.80 0.27 0.02
69_E 23_Q 0.80 0.26 0.02
132_A 50_V 0.80 0.26 0.02
58_G 68_D 0.80 0.26 0.02
38_H 44_K 0.79 0.26 0.02
36_R 58_A 0.79 0.26 0.02
141_Y 19_T 0.79 0.26 0.02
65_S 62_I 0.79 0.26 0.02
122_G 44_K 0.79 0.26 0.02
128_I 62_I 0.78 0.25 0.02
119_V 44_K 0.78 0.25 0.02
156_E 13_I 0.78 0.25 0.02
13_G 18_A 0.78 0.25 0.02
152_N 9_A 0.77 0.24 0.02
64_L 58_A 0.77 0.24 0.02
135_F 34_L 0.77 0.24 0.02
114_K 34_L 0.77 0.24 0.02
135_F 13_I 0.76 0.24 0.02
109_D 7_V 0.76 0.24 0.02
77_D 42_N 0.76 0.23 0.02
30_A 22_V 0.76 0.23 0.02
145_K 13_I 0.76 0.23 0.02
92_I 38_G 0.76 0.23 0.02
138_K 33_N 0.76 0.23 0.02
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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